CLAffinity:A software tool for identification of optimum ligand affinity for competition-based primary screens

[Image: see text] A simplistic assumption in setting up a competition assay is that a low affinity labeled ligand can be more easily displaced from a target protein than a high affinity ligand, which in turn produces a more sensitive assay. An often-cited paper correctly rallies against this assumption and recommends the use of the highest affinity ligand available for experiments aiming to determine competitive inhibitor affinities. However, we have noted this advice being applied incorrectly to competition-based primary screens where the goal is optimum assay sensitivity, enabling a clear yes/no binding determination for even low affinity interactions. The published advice only applies to secondary, confirmatory assays intended for accurate affinity determination of primary screening hits. We demonstrate that using very high affinity ligands in competition-based primary screening can lead to reduced assay sensitivity and, ultimately, the discarding of potentially valuable active compounds. We build on techniques developed in our PyBindingCurve software for a mechanistic understanding of complex biological interaction systems, developing the “CLAffinity tool” for simulating competition experiments using protein, ligand, and inhibitor concentrations common to drug screening campaigns. CLAffinity reveals optimum labeled ligand affinity ranges based on assay parameters, rather than general rules to optimize assay sensitivity. We provide the open source CLAffinity software toolset to carry out assay simulations and a video summarizing key findings to aid in understanding, along with a simple lookup table allowing identification of optimal dynamic ranges for competition-based primary screens. The application of our freely available software and lookup tables will lead to the consistent creation of more performant competition-based primary screens identifying valuable hit compounds, particularly for difficult targets

Since 1843: in the making, 8 January - 7 February 2014

Catalogue published to accompany the exhibition of the same name held at Nottingham Trent University (Newton, Bonington and Waverley buildings) from 8 January-7 February 2014. The exhibition commenced a series of events to celebrate the 170th anniversary of what in 1843 was named the Nottingham School of Design, and is now the School of Art & Design at Nottingham Trent University

Quantitative microdialysis:Experimental protocol and software for small molecule protein affinity determination and for exclusion of compounds with poor physicochemical properties

Quantitative microdialysis is a traditional biophysical affinity determination technique. In the development of the detailed experimental protocol presented, we used commercially available equipment, rapid equilibrium dialysis (RED) devices (ThermoFisher Scientific), which means that it is open to most laboratories. The target protein and test compound are incubated in a chamber partitioned to allow only small molecules to transition to a larger reservoir chamber, then reversed-phase high performance liquid chromatography (RP-HPLC) or liquid chromatography–mass spectrometry (LC–MS) is used to determine the abundance of compound in each chamber. A higher compound concentration measured in the chamber that contains the target protein indicates binding. As a novel, and differentiating contribution, we present a protocol for mathematical analysis of experimental data. We provide the equations and the software to yield dissociation constants for the test compound-target protein complex up to 0.5 mM KD, and we quantitatively discuss the limitations of affinities in relation to measured compound concentrations

PyBindingCurve, simulation, and curve fitting to complex binding systems at equilibrium

[Image: see text] Understanding multicomponent binding interactions in protein–ligand, protein–protein, and competition systems is essential for fundamental biology and drug discovery. Hand-deriving equations quickly become unfeasible when the number of components is increased, and direct analytical solutions only exist to a certain complexity. To address this problem and allow easy access to simulation, plotting, and parameter fitting to complex systems at equilibrium, we present the Python package PyBindingCurve. We apply this software to explore homodimer and heterodimer formations culminating in the discovery that under certain conditions, homodimers are easier to break with an inhibitor than heterodimers and may also be more readily depleted. This is a potentially valuable and overlooked phenomenon of great importance to drug discovery. PyBindingCurve may be expanded to operate on any equilibrium binding system and allows definition of custom systems using a simple syntax. PyBindingCurve is available under the MIT license at https://github.com/stevenshave/pybindingcurve as the Python source code accompanied by examples and as an easily installable package within the Python Package Index

Randomised feasibility trial into the effects of low-frequency electrical muscle stimulation in advanced heart failure patients.

OBJECTIVES: Low-frequency electrical muscle stimulation (LF-EMS) may have the potential to reduce breathlessness and increase exercise capacity in the chronic heart failure population who struggle to adhere to conventional exercise. The study's aim was to establish if a randomised controlled trial of LF-EMS was feasible. DESIGN AND SETTING: Double blind (participants, outcome assessors), randomised study in a secondary care outpatient cardiac rehabilitation programme. PARTICIPANTS: Patients with severe heart failure (New York Heart Association class III-IV) having left ventricular ejection fraction <40% documented by echocardiography were eligible. INTERVENTIONS: Participants were randomised (remotely by computer) to 8 weeks (5×60 mins per week) of either LF-EMS intervention (4 Hz, continuous, n=30) or sham placebo (skin level stimulation only, n=30) of the quadriceps and hamstrings muscles. Participants used the LF-EMS straps at home and were supervised weekly OUTCOME MEASURES: Recruitment, adherence and tolerability to the intervention were measured during the trial as well as physiological outcomes (primary outcome: 6 min walk, secondary outcomes: quadriceps strength, quality of life and physical activity). RESULTS: Sixty of 171 eligible participants (35.08%) were recruited to the trial. 12 (20%) of the 60 patients (4 LF-EMS and 8 sham) withdrew. Forty-one patients (68.3%), adhered to the protocol for at least 70% of the sessions. The physiological measures indicated no significant differences between groups in 6 min walk distance(p=0.13) and quality of life (p=0.55) although both outcomes improved more with LF-EMS. CONCLUSION: Patients with severe heart failure can be recruited to and tolerate LF-EMS studies. A larger randomised controlled trial (RCT) in the advanced heart failure population is technically feasible, although adherence to follow-up would be challenging. The preliminary improvements in exercise capacity and quality of life were minimal and this should be considered if planning a larger trial. TRIAL REGISTRATION NUMBER: ISRCTN16749049

Cardiac structure and function in adolescent Sherpa; effect of habitual altitude and developmental stage

The purpose of this study was to examine ventricular structure and function in Sherpa adolescents to determine whether age-specific differences in oxygen saturation (S

High-intensity interval training in cardiac rehabilitation (HIIT or MISS UK): A multi-centre randomised controlled trial

Background: There is a lack of international consensus regarding the prescription of high-intensity interval exercise training (HIIT) for people with coronary artery disease (CAD) attending cardiac rehabilitation (CR).Aim: To assess the clinical effectiveness and safety of low-volume HIIT compared with moderate intensity steady-state (MISS) exercise training for people with CAD.Methods: We conducted a multi-centre RCT, recruiting 382 patients from 6 outpatient CR centres. Participants were randomised to twice-weekly HIIT (n = 187) or MISS (n = 195) for 8 weeks. HIIT consisted of 10 × 1-minute intervals of vigorous exercise (>85% maximum capacity) interspersed with 1-minute periods of recovery. MISS was 20-40 minutes of moderate intensity continuous exercise (60-80% maximum capacity). The primary outcome was the change in cardiorespiratory fitness (peak oxygen uptake, VO2 peak) at 8-week follow-up. Secondary outcomes included cardiovascular disease risk markers, cardiac structure and function, adverse events, and health-related quality of life.Results: At 8 weeks, VO2 peak improved more with HIIT (2.37 mL.kg-1.min-1; SD, 3.11) compared with MISS (1.32 mL.kg-1.min-1; SD, 2.66). After adjusting for age, sex and study site, the difference between arms was 1.04 mL.kg-1.min-1 (95% CI, 0.38 to 1.69; p = 0.002). Only 1 serious adverse event was possibly related to HIIT.Conclusions: In stable CAD, low-volume HIIT improved cardiorespiratory fitness more than MISS by a clinically meaningful margin. Low-volume HIIT is a safe, well tolerated, and clinically effective intervention that produces short-term improvement in cardiorespiratory fitness. It should be considered by all CR programmes as an adjunct or alternative to MISS

Chemical interrogation of nuclear size identifies compounds with cancer cell line specific effects on migration and invasion

[Image: see text] Background: Lower survival rates for many cancer types correlate with changes in nuclear size/scaling in a tumor-type/tissue-specific manner. Hypothesizing that such changes might confer an advantage to tumor cells, we aimed at the identification of commercially available compounds to guide further mechanistic studies. We therefore screened for Food and Drug Administration (FDA)/European Medicines Agency (EMA)-approved compounds that reverse the direction of characteristic tumor nuclear size changes in PC3, HCT116, and H1299 cell lines reflecting, respectively, prostate adenocarcinoma, colonic adenocarcinoma, and small-cell squamous lung cancer. Results: We found distinct, largely nonoverlapping sets of compounds that rectify nuclear size changes for each tumor cell line. Several classes of compounds including, e.g., serotonin uptake inhibitors, cyclo-oxygenase inhibitors, β-adrenergic receptor agonists, and Na(+)/K(+) ATPase inhibitors, displayed coherent nuclear size phenotypes focused on a particular cell line or across cell lines and treatment conditions. Several compounds from classes far afield from current chemotherapy regimens were also identified. Seven nuclear size-rectifying compounds selected for further investigation all inhibited cell migration and/or invasion. Conclusions: Our study provides (a) proof of concept that nuclear size might be a valuable target to reduce cell migration/invasion in cancer treatment and (b) the most thorough collection of tool compounds to date reversing nuclear size changes specific to individual cancer-type cell lines. Although these compounds still need to be tested in primary cancer cells, the cell line-specific nuclear size and migration/invasion responses to particular drug classes suggest that cancer type-specific nuclear size rectifiers may help reduce metastatic spread

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

Background: The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and their modulators remains a challenge. Here, we report a broadly applicable, multiplexed, miniaturized on-bead technique for real-time monitoring of various ubiquitination-related enzymatic activities. The assay, termed UPS-confocal fluorescence nanoscanning (UPS-CONA), employs a substrate of interest immobilized on a micro-bead and a fluorescently labeled ubiquitin which, upon enzymatic conjugation to the substrate, is quantitatively detected on the bead periphery by confocal imaging.Results: UPS-CONA is suitable for studying individual enzymatic activities, including various E1, E2, and HECT-type E3 enzymes, and for monitoring multi-step reactions within ubiquitination cascades in a single experimental compartment. We demonstrate the power of the UPS-CONA technique by simultaneously following ubiquitin transfer from Ube1 through Ube2L3 to E6AP. We applied this multi-step setup to investigate the selectivity of five ubiquitination inhibitors reportedly targeting different classes of ubiquitination enzymes. Using UPS-CONA, we have identified a new activity of a small molecule E2 inhibitor, BAY 11-7082, and of a HECT E3 inhibitor, heclin, towards the Ube1 enzyme.Conclusions: As a sensitive, quantitative, flexible, and reagent-efficient method with a straightforward protocol, UPS-CONA constitutes a powerful tool for interrogation of ubiquitination-related enzymatic pathways and their chemical modulators, and is readily scalable for large experiments

PuLSE:Quality control and quantification of peptide sequences explored by phage display libraries

The design of highly diverse phage display libraries is based on assumption that DNA bases are incorporated at similar rates within the randomized sequence. As library complexity increases and expected copy numbers of unique sequences decrease, the exploration of library space becomes sparser and the presence of truly random sequences becomes critical. We present the program PuLSE (Phage Library Sequence Evaluation) as a tool for assessing randomness and therefore diversity of phage display libraries. PuLSE runs on a collection of sequence reads in the fastq file format and generates tables profiling the library in terms of unique DNA sequence counts and positions, translated peptide sequences, and normalized 'expected' occurrences from base to residue codon frequencies. The output allows at-a-glance quantitative quality control of a phage library in terms of sequence coverage both at the DNA base and translated protein residue level, which has been missing from toolsets and literature. The open source program PuLSE is available in two formats, a C++ source code package for compilation and integration into existing bioinformatics pipelines and precompiled binaries for ease of use